[Pw_forum] Error optmizing doped graphene

Tue Oct 24 12:39:59 CEST 2017

It might also be a problem of tiny numerical differences, due to different
parallelization/compiler/libraries/phases of the moon, leading the code to
different execution patterns. It has always been hard to pinpoint the
origin of those errors.

Paolo

On Tue, Oct 24, 2017 at 10:45 AM, Giuseppe Mattioli <
giuseppe.mattioli at ism.cnr.it> wrote:

>
> Dear Bhushan
>
> > The calculation has successfully completed on my local server without any
> > error.
>
> On mine too.
>
> It is likely an issue arising from a compiler or a library error, and
> it is of course *very difficult* to correct, because we have no access
> to your hpc facility and such kind of debug is a really time-consuming
> task. I can only suggest you to ask the hpc system administrator, to
> tell him that an application is running fine on your local cluster
> when compiled with a given compiler and linked against a given set of
> libraries, and it is not on the hpc cluster.
>
> HTH
> Giuseppe
>
> Quoting B S Bhushan <ecebhushan at gmail.com>:
>
> > Dear Dr.Giuseppe and Dr. Lorenzo,
> >
> > The calculation has successfully completed on my local server without any
> > error.
> > However, I am not yet sure why I am getting the error on Supercomputer,
> and
> > how to get rid of it.
> >
> > Thank you.
> >
> >
> > On Mon, Oct 23, 2017 at 9:54 PM, B S Bhushan <ecebhushan at gmail.com>
> wrote:
> >
> >> Dear Dr. Giuseppe,
> >>
> >> I have already submitted the same job on a different machine (my local
> >> server) and awaiting the result. So far I have not seen any error, yet
> I am
> >> awaiting the final result.
> >>
> >> The error I posted was actually received when I tried to perform it
> using
> >> a High Performance computing facility.
> >>
> >> I will let you know of the result from my local server.
> >>
> >>
> >> On Mon, Oct 23, 2017 at 9:48 PM, B S Bhushan <ecebhushan at gmail.com>
> wrote:
> >>
> >>> Thank you very much for your support Dr. Lorenzo.
> >>>
> >>> I will try these and let you know the result.
> >>>
> >>> On Mon, Oct 23, 2017 at 9:07 PM, Lorenzo/Eric Paulatto <
> >>> ericpaulatto at gmail.com> wrote:
> >>>
> >>>> Dear B S,
> >>>>
> >>>> I've had a look at your input, I see that the C-N distance is already
> >>>> quite small at the beginning, and become even smaller after a couple
> of
> >>>> iteration; definitely smaller that the core radius of the two
> >>>> pseudopotentials used, which is a typical cause of
> >>>> diagonalisation problems.
> >>>>
> >>>> You should try using some harder pseudopotentials, I've attached two
> >>>> hard pseudopotential fro mthe pslibrary of Andrea Dal Corso (do not
> forget
> >>>> to cite), which should do the trick. Take care of converging the
> cutoff.
> >>>> UPDATE: I'm not attaching the pseudos because they don't pass in the
> list,
> >>>> I'm sending them privately in a minute
> >>>>
> >>>> Please let us know if this solves your problem!
> >>>>
> >>>> kind regards
> >>>>
> >>>> On 23/10/17 15:08, B S Bhushan wrote:
> >>>>
> >>>> Dear Dr. Lorenzo,
> >>>>
> >>>> I think the error is occurring in the 4th optimization step.
> >>>> I have attached the output file for your reference.
> >>>>
> >>>>
> >>>> Awaiting your kind response.
> >>>> B S Bhushan
> >>>> Ph.D Scholar,
> >>>> ABV-IIITM Gwalior, India.
> >>>>
> >>>>
> >>>>
> >>>> On Mon, Oct 23, 2017 at 4:44 PM, Lorenzo Paulatto <paulatz at gmail.com>
> >>>> wrote:
> >>>>
> >>>>> is it at the first structural relaxation step or later? I'm afraid
> that
> >>>>> doing a vc-relax of a small supercell with a defect could cause an
> >>>>> unphysical crunch
> >>>>>
> >>>>> On 21/10/17 18:52, B S Bhushan wrote:
> >>>>>
> >>>>> Dear Expert,
> >>>>>
> >>>>> I was getting the below error while trying to vc-relax a doped
> graphene.
> >>>>> can you please suggest why is it occurring??
> >>>>>
> >>>>>
> >>>>>      iteration #  9     ecut=    30.00 Ry     beta=0.70
> >>>>>      Davidson diagonalization with overlap
> >>>>>
> >>>>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >>>>> %%%%%%%%%%%%%%%%%%%
> >>>>>      Error in routine  cdiaghg (261):
> >>>>>       problems computing cholesky
> >>>>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >>>>> %%%%%%%%%%%%%%%%%%%
> >>>>>
> >>>>>      stopping ...
> >>>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 22
> >>>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 20
> >>>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
> >>>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> Sincerely,
> >>>>>
> >>>>> B S Bhushan,
> >>>>> Ph.D scholar,
> >>>>> ABV-IIITM Gwalior, India.
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> Pw_forum mailing
> >>>>> listPw_forum at pwscf.orghttp://pwscf.org/mailman/listinfo/pw_forum
> >>>>>
> >>>>>
> >>>>> --
> >>>>> Lorenzo Paulatto - Paris
> >>>>>
> >>>>>
> >>>>> _______________________________________________
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> >>>>> http://pwscf.org/mailman/listinfo/pw_forum
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
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> >>>>
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> >>>
> >>>
> >>
>
>
>
> GIUSEPPE MATTIOLI
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> Via Salaria Km 29,300 - C.P. 10
> I-00015 - Monterotondo Scalo (RM)
> Mob (*preferred*) +39 373 7305625
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> E-mail: <giuseppe.mattioli at ism.cnr.it>
>
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-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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